Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KDM6A

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK293 cells
cell line full name
Flp-In T-REx HEK293 (Invitrogen, R78007)
cell type
human embryonic kidney cells
chip antibody
rabbit α-UTX/KDM6A (Cell Signaling Technology, 33510S)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After sequential lysis of the crosslinked cells in Lysis Buffer 1 and Lysis Buffer 2, the nuclear pellet was sonicated in Lysis Buffer 3 with a probe sonicator (Fisher Scientific Model 705 Sonic Dismembrator) at output level 55 (27–33 W) for 16 cycles with each cycle constituting of a 30 sec sonication on followed by a 60 sec off. For each ChIP, 100 μL Protein G Dynabeads (Invitrogen, 10003D) slurry and 10 µg of antibody was used. Chromatin incubation with antibody was carried out at 4°C with end-to-end rotation for 4-6 hours. DNA was quantified using the Quant-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, P11496). Libraries were prepared with the KAPA HyperPrep Library Kit (Roche, 07962363001) and analyzed for insert size distribution with the High Sensitivity DNA Kit (Agilent, 5067–4626) on a 2100 Bioanalyzer or the High Sensitivity D1000 ScreenTape Assay (Agilent, 5067–5584, 5067–5585, 5067–5587, 5067–5603) on a 4200 TapeStation. Libraries were quantified using the Quant-iT PicoGreen dsDNA Assay. HiSeq 2500, HiSeq 4000, or NovaSeq 6000 System (all from Illumina) was used.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
13326179
Reads aligned (%)
95.7
Duplicates removed (%)
11.0
Number of peaks
38042 (qval < 1E-05)

hg19

Number of total reads
13326179
Reads aligned (%)
95.5
Duplicates removed (%)
11.0
Number of peaks
37965 (qval < 1E-05)

Base call quality data from DBCLS SRA